Journal Article

Comparative genome analysis of central nitrogen metabolism and its control by GlnR in the class Bacilli

Hagemeijer, Yanick, Overmars, Lex, Siezen, Roland J, Koenders, Eric, Francke, Christof, de Vos, Willem M, Kormelink, Tom Groot

2012

Overview

Background The assimilation of nitrogen in bacteria is achieved through only a few metabolic conversions between alpha-ketoglutarate, glutamate and glutamine. The enzymes that catalyze these conversions are glutamine synthetase, glutaminase, glutamate dehydrogenase and glutamine alpha-ketoglutarate aminotransferase. In low-GC Gram-positive bacteria the transcriptional control over the levels of the related enzymes is mediated by four regulators: GlnR, TnrA, GltC and CodY. We have analyzed the genomes of all species belonging to the taxonomic families Bacillaceae, Listeriaceae, Staphylococcaceae, Lactobacillaceae, Leuconostocaceae and Streptococcaceae to determine the diversity in central nitrogen metabolism and reconstructed the regulation by GlnR. Results Although we observed a substantial difference in the extent of central nitrogen metabolism in the various species, the basic GlnR regulon was remarkably constant and appeared not affected by the presence or absence of the other three main regulators. We found a conserved regulatory association of GlnR with glutamine synthetase ( glnRA operon), and the transport of ammonium ( amtB-glnK ) and glutamine/glutamate (i.e. via glnQHMP , glnPHQ , gltT , alsT ). In addition less-conserved associations were found with, for instance, glutamate dehydrogenase in Streptococcaceae, purine catabolism and the reduction of nitrite in Bacillaceae, and aspartate/asparagine deamination in Lactobacillaceae. Conclusions Our analyses imply GlnR-mediated regulation in constraining the import of ammonia/amino-containing compounds and the production of intracellular ammonia under conditions of high nitrogen availability. Such a role fits with the intrinsic need for tight control of ammonia levels to limit futile cycling.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Amino Acid Sequence / Ammonia / Ammonia - metabolism / Ammonium / Analysis / Animal Genetics and Genomics / asparagine synthetase / Bacillaceae / Bacillaceae - classification / Bacillaceae - enzymology / Bacillaceae - genetics / Bacillus (Bacteria) / Bacteria / Bacterial Proteins - genetics / Bacterial Proteins - metabolism / Bacteriology / Binding Sites / Biomedical and Life Sciences / Chromosomes / Dehydrogenase / DNA - metabolism / Enzymes / escherichia-coli / Gene Expression Regulation, Bacterial / Genetic aspects / Genome, Bacterial / Genomes / Genomics / Glutamate / Glutamate-Ammonia Ligase - genetics / Glutamate-Ammonia Ligase - metabolism / Glutamine / Glutamine synthetase / glutamine-synthetase gene / Lactobacillaceae / Lactobacillaceae - enzymology / Lactobacillaceae - genetics / lactobacillus-plantarum / lactococcus-lactis / Leuconostocaceae - enzymology / Leuconostocaceae - genetics / Life Sciences / Ligases / Listeria - enzymology / Listeria - genetics / Metabolism / Microarrays / Microbial Genetics and Genomics / Molecular Sequence Data / Nitrogen / Nitrogen - metabolism / nucleotide-sequence / Physiological aspects / Plant Genetics and Genomics / Proteins / Proteomics / reductase/2,3-butanediol dehydrogenase / Repressor Proteins - genetics / Repressor Proteins - metabolism / Research Article / Staphylococcaceae - enzymology / Staphylococcaceae - genetics / Streptococcaceae / Streptococcaceae - enzymology / Streptococcaceae - genetics / streptococcus-mutans / subtilis ureabc operon / transcription factor tnra